Krystyna Szczepaniak

Infrared studies and the effect of ultraviolet irradiation on the tautomers of 9-methylguanine isolated in an argon matrix

Abstract The infrared spectrum of 9-methylguanine isolated in an argon matrix at 15 K, and the effect of ultraviolet irradiation on this spectrum, are presented and discussed. These studies prove that the amino-oxo and amino-hydroxy tautomers of 9-methylguanine are present in the matrix and allow the separation of the overlapping spectra of these forms. The concentrations of both tautomers in the matrix are approximately the same while in solutions and in crystal only the amino-oxo form is present. This finding may have important biological implications related to the possible appearance of guanosine-(amino-hydroxy)-thymidine base pairs.

Tautomerism of nucleic acid bases and the effect of molecular interactions on tautomeric equilibria

Abstract The change in tautomeric equilibria of purine and pyrimidine bases which may occur as a result of changes from an inert to polar environment of the base is examined in a general way. The contributions to the interaction energy between two molecules of 2-oxo-5-chloro-pyrimidine are compared specifically with those for 2-hydroxy-5-chloropyrimidine to show the influence of such an interaction on the relative stability of the oxo and hydroxy tautomeric forms. Similar effects are expected to change the relative order of stabilities of tautomers of purines and pyrimidine bases as a result of their interactions with their environment. The advantages of infrared studies of these equilibria for matrix isolated bases to provide information about the isolated bases, are discussed, and the extensive results from such studies over the past 14 years are reviewed. This review concentrates on studies of the biologically significant nucleic acid bases (1-methyluracil, 1-methylcytosine, 9-methyladenine and 9-methylguanine (9-MG) and several related model compounds). The technique for these studies is reviewed and illustrated with specific examples. For all of these bases except the guanosine analog 9-MG, only one tautomeric form is found to occur in the inert matrix environment, and it is the same form found for the base in polar solutions. However, for 9-MG the normal “oxo” tautomer (G) is found to be in approximately 1:1 equilibrium with the rare “hydroxy” tautomer (G*) in the inert (Ar or N2) gas matrix. These results contrast sharply with the studies of guanine residue in more polar environments where only the oxo form is found. The possible biological significance of this finding may be considerable, since G* will form a base pair with thymine rather than cytosine, possibly leading to spontaneous mutation. Finally, recent results from theoretical ab initio calculations of relative stabilities of the nucleic acid bases are reviewed and summarized. These results show the importance of making such calculations with large enough basis sets and estimate the effects of including electron correlation and correcting for zero point vibrational energies.

Infrared spectra and tautomerism of 5-fluorocytosine, 5-bromocytosine and 5-iodocytosine. Matrix isolation and theoretical AB initio studies

Abstract The infrared (IR) spectra of 5-fluorocytosine (5FC), 5-bromocytosine (5BrC) and 5-iodocytosine (5IC) all isolated in an argon matrix at 15 K are presented and discussed. Vibrational assignments are proposed based on ab initio quantum mechanical calculations (3–21G basis set) of the IR frequencies and intensities for the amino-oxo and amino-hydroxy tautomers of 5FC. The IR spectra prove that the amino-hydroxy tautomer strongly dominates in an inert matrix for all the 5-halogenated cytosines studied, in sharp contrast with the dominance of the amino-oxo form in polar media. From the experimental absorbances and theoretical molar absorption coefficients the equilibrium constants. K (h/o), and the difference in the energies of the amino-hydroxy and amino-oxo tautomers are estimated. The value of 5FC agrees very well with the energy difference calculated using a 6–31G** basis set (single point) and 3–21G optimized geometry, corrected for the difference in the zero-point vibrational energy.

The tautomeric equilibria of thioanalogues of nucleic acids: spectroscopic studies of 2-thiouracils in the vapour phase and in low temperature matrices

Abstract The IR absorption spectra in the NH, OH and SH stretching regions of 2-thiouracil and its N 1 -, N 3 -, O - and S -alkyl derivatives, isolated in the vapour phase and also isolated in inert low temperature matrices, and the UV absorption spectra of those compounds measured in the vapour phase are presented and discussed. These spectra establish unambiguously the tautomeric forms of these systems which are found for isolated molecules. 2-Thiouracil as well as its N 1 - and N 3 -methylated derivatives exists in the inert matrix and in the vapour phase only in the oxo-thione tautomeric form; this same form is found for these molecules in solutions and in the solid phase. In contrast, 2-methylthiouracil isolated in inert matrices and in the vapour adopts both the 4-oxo and the 4-hydroxy tautomeric forms, with an equilibrium constant K (oxo = hydroxy) of 1.2, while it exists only as the 4-oxo form in solutions and in the solid. The 4-neopentoxy derivative of 2-thiouracil, when isolated in an inert matrix, is found to be in the mercapto form only, while the thione form is dominant in the solid phase and in solution.

Ab initio theoretical and matrix isolation experimental studies of hydrogen bonding: vibrational consequences of proton position in 1:1 complexes of HCl and 4-X-pyridines

Abstract Ab initio calculations at the MP2/6–31 + G(d, p) level have been performed to determined the structures, binding energies, and vibrational spectra of a series of 1:1 HCl:4-X-pyridine complexes with X = H, Ch 3 , NH 2 , OH, F, Cl, CN, CHO, Li, Na, O − and S − . The substituents include both electron donating and electron withdrawing groups which systematically alter the basicity of the pyridine nitrogen. The hydrogen bonds in these complexes span the range of proton positions, including ClH…N hydrogen bonds between neutral molecules, Cl − … + HN hydrogen bonds between ion pairs, and proton-shared Cl…H…N hydrogen bonds. Emphasis is placed on the relationship between proton position and vibrational spectrum, particularly the vibrational bands associated with proton motion.

Ab initio theoretical and matrix isolation experimental studies of hydrogen bonding. IV. The HBr:pyridine complex

Abstract Experimental matrix isolation studies have been performed for the HBr/pyridine/argon system at 10 K to obtain the infrared spectrum of the isolated one-to-one HBr:pyridine complex. The experimental spectrum is consistent with those for complexes with proton-shared hydrogen bonds. Details of the experimental procedure and the analysis of the experimental spectrum are presented. Comparison of the experimental IR spectrum of the complex with the harmonic spectrum computed at MP2/6–31+G(d,p) shows that both theory and experiment agree that this complex is stabilized by a proton-shared hydrogen bond. However, discrepancies exist between computed and experimental frequency and intensity patterns. Single point calculations at MP2/6–31+G(d,p) for displacements along the normal coordinate for proton stretching produced a potential energy curve which is strongly anharmonic. The anharmonic frequency for the proton stretching mode was estimated from this curve. The ratio of the anharmonic to harmonic frequency yielded an effective force constant. The re-computed spectrum obtained with this constant is in excellent agreement with experiment.

Intermolecular interactions and tautomerism of nucleic acid bases and their analogues

Abstract The structures and stabilization energies of guanine—cytosine, guanine—thymine and adenine—thymine base pairs formed by “normal” amino-oxo and “rare” amino-hydroxy tautomers of guanine and the “normal” tautomers of adenine and thymine are studied using a combined quantum-mechanical approach, an ab initio calculation for relative stabilities of the isolated tautomers together with a calculation of intermolecular interaction energies using a multipolar expansion method developed by Claverie and co-workers. It is shown that the interaction between the components of the base pairs decreases the relative stability of the pairs involving “rare” tautomers of guanine; for the isolated molecules the stability of both tautomers of guanine is found to be approximately the same. Our calculations include the base pairs formed by the “rare” hydroxy tautomer of guanine, whose existence has been reported in recent experimental studies of guanines isolated in an inert low-temperature matrix. Calculations for this amino-hydroxy form of guanine serve as a model for interactions of O 6 -methylguanine with pyrimidine bases.

Quantum-mechanical studies of the structures of cytosine dimers and guanine—cytosine pairs

Abstract The structures of cytosine—cytosine dimers and guanine—cytosine pairs formed between different tautomeric forms of the bases are studied using a combined quantum-mechanical approach: an ab initio calculation for relative stabilities of the isolated tautomers together with a calculation using Claveries method for predicting intermolecular interaction energies. It is shown that the interaction between the bases in the complex changes the relative stability of the individual tautomers; in particular the probability of in the complexes the occurrence in the complexes of the “rare” tautomers of cytosine and guanine is found to be lower.

INFRARED AND RAMAN SPECTRA OF ALKYLATED GUANINE DERIVATIVES

Abstract The infrared and Raman spectra of 9-methylguanine, 9-ethylguanine and 1,9-dimethylguanine in the solid state are reported and discussed. Hydrogen bonds in the solid guanine derivatives bring about strong perturbations in the spectra from those of the isolated molecules. The results are discussed in terms of structural data from X-ray diffraction studies. The infrared spectra of guanine derivatives are compared with the spectra of these molecules isolated in low temperature argon matrices. This comparison allows the determination of the frequency changes due to hydrogen bonding and the interpretation of their vibrational spectra in terms of the normal modes calculated for the isolated guanine molecule.

Experimental and Ab Initio Quantum Mechanical Studies of the Vibrational Spectra of Isolated Pyrimidine Bases

A review is presented of experimental studies of infrared and Raman spectra of thymine isolated in an argon matrix at about 12 K. The experimental techniques for study of the vibrational spectra of matrix-isolated pyrimidines are described, and the reasons for such studies are illustrated by comparison of the infrared and Raman spectra of matrix-isolated thymine with spectra in the solid phase. Comparison of the infrared spectrum of p-quinone isolated in an argon matrix with that for the molecule in the gas phase establishes that the spectra of matrix-isolated molecules are expected to be very similar to those for the gas phase, except for the lack of rotational structure in the matrix spectra. On the other hand, hydrogen bonding in the solid phase has a profound effect on the infrared spectrum, with much smaller effect on the Raman spectrum. Ab initio quantum-mechanical calculations at the HF/6–3 lG(d) level made for the isolated molecules are compared with the experimental spectra and their application to the interpretation of the latter is illustrated.